tbuckley/cabot-search huggingface dataset:
MODL-22. DEVELOPMENT OF A PATIENT-DERIVED MODEL BIOBANK TO PROVIDE AN ACCURATE TOOL DECIPHERING BRAIN TUMOR INITIATION, PROGRESSION, AND THERAPEUTIC RESISTANCE
Authors: Marlène Deschuyter, Thibaut Wolf, Benoit Lhermitte, Damien Reita, Quentin Fuchs, Marina Pierrevelcin, Sophie Foppolo, Monique Dontenwill, Natacha Entz-Werlé
Journal: Neuro-Oncology (2023)

Abstract Brain cancers are the most incident and deadliest tumor types in pediatric and young adult populations. Among them, several histotypes are characterized by their molecular drivers and co-alterations currently guiding our therapeutic strategies. Due to inter- and intra-tumoral heterogeneity, those tumors are becoming rapidly chemo- and radioresistant. To encompass all their intrinsic and extrinsic mechanisms of therapeutic resistances, there is an urgent need to generate accurate brain tumors’ modeling to predict therapeutic responses. Patient-derived cell lines (PDCL) remain for now the most reliable model to estimate and mimic evolutive situation. Main difficulties rely on the derivation methods themselves (2D vs. 3D, in vitro vs. in vivo), but also on the methods to validate their molecular similarities comparatively to the primary tumors. Here we collected, through the PEDIAMODECAN program, 104 fresh brain tumors (e.g., 23 pilocytic astrocytomas (PA), 3 low-grade gliomas (LGG), 13 supra-tentorial high-grade gliomas and 10 DIPG/DMGs, 19 ependymomas, 19 medulloblastomas, 17 other rare entities) to generate PDCL and patient-derived xenografts (PDX). Using Next-Generation Sequencing (NGS), methylome assay and RNA sequencing, we were in capacity to underline similarities with initiated samples. Looking to derivation itself, we successfully maintained 80% samples in 2D cultures and 54% were derived in PDX. As expected, the PA/LGG group shows the higher percentage of failure of PDX generation (90%) and all established PA/LGG PDCLs were limited to a low number of passages. Nevertheless, for high-grade subtypes, PDX generation rate increased to 85,7%. No correlation was observed between derivation success and time between surgical removal and dissociation process. Whereas PDX histology was reproducing the same microscopic features than the primary tumors, methylome assay proves to be a good method to confirm original histotype group. Furthermore, those primary models afford a large biobank reproducing the diversity of pediatric brain tumors and were easily drug screened.
PATH-60. BRAIN TUMORS: FROM ONCOSTREAMS TO LIQUID CRYSTALS
Authors: Pedro Lowenstein, Syed M Faisal, Anna Argento, Andrea Comba, Sebastien Motsch, Carles Blanch-Mercader, Maria Castro
Journal: Neuro-Oncology (2023)

Abstract High grade gliomas (HGG) are the most common, destructive, and varied of all malignant brain tumors. HGG are heterogeneous at the histological, cellular, and molecular level, which makes them hard to study and treat. One particular tumor pathological differentiation is mesenchymal differentiation, containing oblong, motile cells. We recently noted distinct fascicles of elongated, aligned, mesenchymal-like cells in mouse and human gliomas, which we denote as oncostreams. Time-lapse confocal microscopy in ex vivo slices, and in in vivo two photon imaging, indicated that cells in oncostreams are motile. Oncostream motility was classified based on cellular orientation. The molecular characteristics of oncostreams were determined by laser capture microdissection, RNA-sequencing, and bioinformatics. 43 genes were differentially expressed; COL1A1 was overexpressed in oncostreams. Inhibition of COL1A1 in mouse gliomas, using the Sleeping Beauty transposon model, reduced oncostreams, tumor aggressiveness, proliferation, tumor vasculature, and collective glioma invasion. More recently, we elucidated that glioma cell growth in vitro, and potentially in vivo displays domains of nematic orientation (oncostreams) and topological defects, suggesting that gliomas are organized as liquid crystals. Topological defects are singularities of local orientation, and characteristic of liquid crystals. Further, studies of gliomas in vivo, suggest the presence of ±1/2 topological defects. Thus, nematic orientation and topological defects are present in brain tumors in vitro and in vivo. This provides support for our hypothesis that brain tumors are organized as active liquid crystals. As topological defects have been exploited to alter liquid crystal behavior, we hypothesize that manipulating brain tumor liquid crystalline behavior will be of therapeutic importance. Comba et al. (2022) Spatiotemporal analysis of glioma heterogeneity reveals COL1A1 as an actionable target to disrupt tumor progression. Nature Communications: Wood et al. (2023) Scale-free correlations and potential criticality in weakly ordered populations of brain cancer cells. Science Advances (in press).
TMIC-14. CLEC5A REGULATES TAM POLARIZATION, TME IMMUNOSUPPRESSION AND DISEASE PROGRESSION IN GLIOBLASTOMA
Authors: Jiabo Li, Xuya Wang, Luqing Tong, Steven Markwell, Ling-Kai Shih, Cheryl Olson, Tatiana Carneiro-Lobo, Xunjun Yang, Daniel Brat
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma, IDH-wildtype (WHO grade 4) is the most common primary malignant brain tumor of adults and is characterized by an immunosuppressive tumor microenvironment (TME) and poor clinical outcomes. CLEC5A is a gene whose expression enhances immune response in inflammatory and infectious diseases, yet its role in GBM immune regulation is unclear. Seurat analysis of scRNA-seq data and CIBERSORTx analysis of GBM RNA-seq data showed that tumor-associated macrophages (TAMs) account for the large majority of immune cells in the GBM, and that CLEC5A expression in this population (CD163+) is highest in hypoxic, peri-necrotic zones. Notably, among all immunosuppressive TAM related genes, CLEC5A expression shows the strongest association with poor clinical outcomes. Monocytes (THP-1 cells) exposed to GBM conditioned media exhibit enhanced CLEC5A and CD163 expression. Moreover, overexpression of CLEC5A by THP-1 cells enhances TAM polarization, migration toward glioma cells, and increased secretion of cytokines that mediate immunosuppression, including IL-1β, IL-4, IL-6, IL-8, IL-10 and IL-13. CLEC5A triggers the activation and phosphorylation of the Syk-Jak2-STAT3 signaling through its interaction with Syk, offering a potential therapeutic intervention. In addition, CLEC5A acts as a receptor, binding to Podoplanin (PDPN) expressed on GBM cells in the peri-necrotic TME, triggering CLEC5A-Syk-JAK-STAT3 signaling and highlighting their role in TAM polarization and the immunosuppressive TME. In vivo, silencing CLEC5A delayed glioma growth, prolonged survival and was associated with reduced CD163 and neoplastic Ki-67 expression. Collectively, we found that CLEC5A expression by TAMs is regulated by PDPN-CLEC5A-Syk-JAK-STAT3 signaling and enhances TAM polarization, TME immunosuppression and GBM growth.
MODL-25. INTERNAL CAROTID INJECTION MODEL OF BRAIN METASTASIS DESCRIBES LEPTOMENINGEAL DISEASE
Authors: Sophia Chernikova, Sheila Tsau, Yuelong Wang, Griffin Hartmann, Dina Polyak, Hriday Bhambhvani, Sai Saroja Kolluru, Thy Trinh, Kerriann Casey, Eli Johnson, Ian Connolly, Lawrence Recht, G-One Ahn, Seema Nagpal, Stephen Quake, J Martin Brown, Melanie Hayden Gephart
Journal: Neuro-Oncology (2023)

Abstract Leptomeningeal disease (LMD), the most aggressive form of central nervous system (CNS) metastasis in which cancer cells infiltrate leptomeninges, is universally and rapidly fatal due to poor detection and no effective treatment. Treatment of LMD is challenged by the diffuse nature of the disease, low specificity of detection, poor drug penetration into CNS and high neurotoxicity. LMD is a heterogeneous disease: co-existence of leptomeningeal spread and parenchymal brain metastases in not uncommon, and LMD tumors vary in size and may be found at various locations throughout entire neuroaxis. Radiographic detection (i.e., MRI) works well for big “bulky” metastases but may produce normal results in patients with active disease identified by cerebrospinal fluid (CSF) tap. This spatial and morphological heterogeneity of LMD may ultimately be responsible for a varied and limited therapy response. Mechanistic and translational studies of LMD are hampered by the lack of adequate in vivo models that recapitulate the consecutive steps of LMD progression separate from systemic disease. In this study, we show that the internal carotid (ICA) injection of tumor cells, which is widely used to model brain metastasis, produces leptomeningeal spread. The ICA injection of various tumor cell lines faithfully recapitulated the stages, heterogeneity, and spatial distribution of human LMD. While some cell lines demonstrated clear preference for growth in brain parenchyma, they still had a measurable population of cells within the leptomeninges. Most bulky LMD metastases formed and grew near fenestrated endothelium, where the direct access to blood might support tumor growth and survival. A population not associated with the fenestrated endothelium consisted mostly of single non-dividing non-hypoxic cells. This diffuse cancer spread limited the efficacy of standard whole-brain radiation therapy. Thus, leptomeningeal spread should be taken into account when interpreting the data from the ICA model that is widely used to study brain metastasis.
INNV-36. ULTRA-FAST DEEP-LEARNED CNS TUMOR CLASSIFICATION USING NANOPORE-SEQUENCING DURING SURGERY
Authors: Pieter Wesseling, Carlo Vermeulen, Marc Pages-Gallego, Lennart Kester, Mariëtte Kranendonk, Niels Verburg, Philip de Witt Hamer, Evert-Jan Kooi, Luuk Dankmeijer, Jasper van der Lugt, Kirsten Van Baarsen, Eelco Hoving, Bastiaan Tops, Jeroen De Ridder
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Preoperative imaging and intraoperative histological analysis provide important guidance during CNS tumor surgery but are not always precise enough. Also, the diagnosis of CNS tumors increasingly requires a combination of morphological and molecular analysis. Illumina DNA methylation array analysis provides information on hundreds of thousands of methylation sites genome-wide but is relatively time-consuming and expensive. Nanopore sequencing enables real-time generation of an increasingly precise methylation profile. AIM: To exploit the potential of nanopore sequencing as a tool for intraoperative molecular diagnostics of CNS tumors. METHODS We developed Sturgeon, a patient-agnostic, transfer-learned neural network approach. Sturgeon leverages publicly available Illumina 450K DNA methylation profiles to simulate millions of nanopore sequencing experiments, which were used to train and validate classifier models. Subsequently, snap-frozen archival samples of 50 CNS tumors were analyzed, as well as fresh tumor samples of an additional 25 CNS tumors intraoperatively. RESULTS Sturgeon delivers models capable of classifying 81 different CNS tumor types based on relatively sparse, randomly distributed nanopore sequencing data. Sturgeon was able to suggest within 40 minutes after the start of sequencing the correct diagnosis with high confidence in 45 out of 50 archival CNS tumor samples; in the remaining cases Sturgeon abstained from a diagnosis. In the real-life scenario, in 18 out of 25 cases (72%) the suggested diagnosis was correct, and in 7 cases the required confidence threshold was not reached (mostly because of low tumor cell percentage). Importantly, the Sturgeon models are portable, work across patients and sequence depths, and require less than a minute of computation on a laptop CPU. CONCLUSIONS Intraoperative nanopore sequencing can assist neurosurgical decision making and opens avenues for starting tumor-specific therapy already during operation. Furthermore, this diagnostic approach has the potential to reduce the costs of methylation profiling analysis and speed-up the multidisciplinary decision-making process.
STEM-14. TARGETING HAUSP IN GLIOMA STEM CELLS INHIBITS MALIGNANT GROWTH AND OVERCOMES RADIORESISTANCE OF GLIOBLASTOMA
Authors: Zhi Huang, Lian Wu, Qian Huang, Kui Zhai, Justin Lathia, Jeremy Rich, Jennifer Yu, Shideng Bao
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma (GBM) is the most lethal and common type of primary brain tumor highly resistant to current treatments including radiotherapy. GBM contains heterogeneous cancer cells including glioma stem cells (GSCs) that promote malignant growth and therapeutic resistance, indicating that targeting GSCs may effectively improve GBM therapy. Here, we show that HAUSP (USP7, a deubiquitinase) is preferentially expressed by GSCs in the perivascular niches in human GBMs. Disrupting HAUSP by shRNA or its inhibitor P22077 promoted GSC differentiation, impaired GSC growth, and potently inhibited GBM malignant growth, indicating that HAUSP is required for maintaining the self-renewal and tumorigenic potential of GSCs. Moreover, pharmacological inhibition of HAUSP synergized with irradiation (IR) to suppress GBM tumor growth, suggesting that targeting HAUSP may effectively overcome GSC-driven radioresistance to improve therapeutic efficacy for GBM. Our findings uncover a novel role of HAUSP in maintaining GSC phenotypes and tumorigenic potential, and thus offer a promising druggable target for developing anti-GSC therapeutics to improve GBM treatment. Furthermore, our preclinical data suggest that inhibiting HAUSP alone or in combination with IR may prolong the survival of GBM patients.
NCOG-06. BEVACIZUMAB ALONE VERSUS BEVACIZUMAB PLUS IRINOTECAN IN PATIENTS WITH RECURRENT GLIOBLASTOMA: A NATIONWIDE POPULATION-BASED STUDY
Authors: Yeonhu Lee, Tae Hoon Roh, Se-Hyuk Kim
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION There is no established treatment for recurrent glioblastoma. For the treatment of recurrent glioblastoma, the antiangiogenic antibody, bevacizumab, is used either alone or in combination with Irinotecan. This study aimed to compare the survival of patients receiving bevacizumab monotherapy (BEV) and those receiving bevacizumab plus irinotecan combination therapy (B+I) in recurrent glioblastoma (GBM), using a nationwide population-based dataset. METHODS Patients matching the ICD code C71.x were screened from the national database. From January 2008 to November 2021, 846 patients who had undergone surgery or biopsy and received concurrent chemoradiotherapy with Temozolomide were included. Of these, 450 received BEV, while 396 received B+I. The patients' demographic characteristics, inpatient stay duration, prescription frequency, and survival outcomes were compared between the two groups. RESULTS The median overall survival from initial surgery was 22.60 months (9% CI: 20.50 – 24.21) and 20.44 months (95% CI: 18.55 – 22.60) in the BEV and B+I groups, respectively (p=0.5079, log rank test). The BEV group was older and had a higher percentage of females compared to the B+I group. Younger age, female gender, and having surgery rather than biopsy were associated with better prognosis. CONCLUSION This study found no significant difference in overall survival between bevacizumab alone versus bevacizumab plus irinotecan combination therapy in patients with recurrent GBM. Considering the additional potential toxicity associated with irinotecan, bevacizumab monotherapy may be a suitable treatment option.
MODL-24. NEUROIMMUNE-COMPETENT HUMAN BRAIN ORGANOID MODEL FOR STUDYING BRAIN TUMOR INVASION
Authors: Katharina Sarnow, Emma Majercak, Ishraq Haque, Xin Tang
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive pediatric brain tumor with a very poor prognosis (&amp;lt; 12 months survival). There is currently no effective treatment for DIPG. Complete surgical resection of DIPG is difficult due to its skull base location and infiltrative growth pattern. Gaining insights into the invasion process of the DIPG cells and their interaction with brain cells in the tumor microenvironment, such as microglia - the brain's primary immune cells, may guide the development of effective treatment strategies to halt or even reverse disease progression. To build a clinically relevant model for studying the microglia/tumor interaction in a 3D human tissue context, we developed a neuroimmune-competent brain organoid/DIPG fusion model system. METHODS Human embryonic stem cell derived-neural progenitor cells (NPCs) and -GFP-labelled human myeloid precursor cells were combined to form microglia-containing organoids (MiCBOs) through self-assembly and co-development over two months. Using two-photon live imaging, we characterized the distribution and motility of microglia in MiCBOs and corroborated these results with immunofluorescence staining and single-cell RNA-Sequencing (scRNA-Seq). Tumor cell invasion and interaction with microglia in the brain organoids were assessed by confocal microscopy as well as immunofluorescence stainings. RESULTS The human microglia in MiCBOs are viable, widely distributed, actively motile, and highly resemble those in the human brain. Confrontation experiments of the MiCBO with DIPG spheroids enable quantitative characterization of the invasion patterns for different cell lines under various conditions. CONCLUSION Our MiCBOs represent a valuable model for studying tumor cell invasion within a neuroimmune-competent human tissue context. Ongoing experiments with different primary DIPG cell lines as well as genetically engineered microglia will deliver more detailed insights into the invasion patterns of tumor cells into brain tissue and shed light on tumor cell/microglia interplay during the DIPG invasion process.
NCOG-05. TREATMENT STRATEGY AND SURVIVAL ANALYSIS OF PATIENTS WITH PRIMARY ADULT-TYPE DIFFUSE GLIOMA IN THE MOLECULAR ERA: A PROSPECTIVE COHORT STUDY FROM THE CGGA NETWORK
Authors: Kenan Zhang, Guanzhang Li, Shengyu Fang, Wei Zhang, Anxin Wang, Tao Jiang
Journal: Neuro-Oncology (2023)

Abstract IMPORTANCE The fifth edition of the WHO Classification of Tumors of the Central Nervous System (CNS) marks the entry of the diagnosis and treatment of diffuse glioma into the molecular era. The clinical implications of this landmark change in primary adult-type diffuse glioma need to be revealed. OBJECTIVE To reveal the clinical prognostic factors of adult diffuse glioma under the WHO CNS 5 classification. DESIGN, SETTING, AND PARTICIPANTS In this clinical-based prospective observational registration study, 3,308 glioma patients from 3 major neurosurgical centers were enrolled between Mar. 2005 to Jun. 2021. After excluding patients who did not meet the inclusion criteria, 1,099 primary adult-type diffuse glioma patients were eligible for inclusion in this study. Student t-test, Chi-squared test, and ANOVA were used for differential analysis. Kaplan-Meier curve and univariate and multivariate Cox regression analyses were used for survival analysis. MAIN OUTCOMES AND MEASURES Totally, 1,099 patients diagnosed with primary adult-type diffuse glioma were included in this study. The male-to-female ratio is about 1.4-1.5 to 1. The mean age at diagnosis for astrocytoma, IDH-mutant, oligodendroglioma, IDH-mutant and 1p/19q-codeleted and glioblastoma, IDH-wildtype were 39.0, 40.0, and 53.0 years, respectively. In astrocytoma, preoperative epilepsy, WHO grade, MGMT promoter methylation status, the extent of resection, and postoperative comprehensive treatment were independently associated with overall survival. For oligodendroglioma, gender, WHO grade, and extent of resection were associated with overall survival. As for glioblastoma patients, gender, age at diagnosis, preoperative KPS, preoperative epilepsy, the extent of resection, and postoperative comprehensive treatment were prognostically correlated. CONCLUSIONS AND RELEVANCE Patients in distinct molecular subtypes showed different epidemiological features and were associated with different clinical prognostic factors.
MODL-45. UNDERSTANDING OLIGODENDROCYTE PROGENITOR CELL CONTRIBUTION TO GLIOMAGENESIS USING A NOVEL PHARMACOGENETIC ABLATION TOOL
Authors: Lulu Xing, Hope Lancero, Dolores Hambardzumyan, Tobias Merson, Claudia Petritsch
Journal: Neuro-Oncology (2023)

Abstract In the central nervous system (CNS), gliomas represent almost 50% of all pediatric tumors and due to their complex histological and biological heterogeneity, aggressive standard treatment consisting of surgery and chemoradiotherapy remains ineffective. As a result, more biologically based therapies are urgently needed and this requires a deeper knowledge of the etiology and biology of gliomas, which can arise from oligodendrocyte progenitor cells (OPCs). OPCs are the most proliferative cell type in the CNS, and upon oncogenic mutations in OPCs, they exhibit defective asymmetric divisions with a concomitant increase in symmetrical renewal, leading to aberrant growth of OPCs prior to malignancy. Although OPC-like cells frequently found in human glioma significantly contribute to tumor heterogeneity and malignancy, how resident tumor-infiltrating OPCs functionally integrate into the tumor cell networks within the tumor microenvironment remains unknown. However, in order to address this critical gap in knowledge of the field, a novel mouse model of conditional OPC ablation must be used to overcome methodological challenges of most current approaches that often result in partial and transient OPC ablation, which limits our understanding of long-term function of OPCs. Here, we have successfully developed a novel pharmacogenetic model of conditional OPC ablation, eliminating 98.6% of all OPCs throughout the mouse brain for up to 12 days post ablation. This novel mouse model of complete OPC ablation can be combined with intracranial injection of tumor cells in order to reveal the longitudinal and spatial functional roles and the necessity for resident OPCs in the tumor context. Understanding the OPC-tumor cell crosstalk by using our state-of-the-art approach at both cellular and molecular levels will have significant clinical implications for improving treatment for patients with pediatric gliomas.